CLCN4 p.Phe319fs
c.957_958del · VCV4730557
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 13 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP 0.42, phastCons 0.001 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CLCN4
- Protein
- p.Phe319fs
- Coding
- c.957_958del
- MANE Select
- NM_001830
- Type
- Deletion
- Location
- chrX:10208156 (GRCh38)
- Structure
- AlphaFold pLDDT 84.66
Similar variants
- CLCN4 p.Phe319Ser Uncertain significance ★ ⚠ same residue
- CLCN4 c.763-13_763-10del Uncertain significance ★★ same type
- CLCN4 c.1390-19_1390-18del Likely benign ★★ same type
- CLCN4 c.1577-7_1577-6del Likely benign ★★ same type
- CLCN4 c.1975+8_1975+9del Likely benign ★★ same type
- CLCN4 p.Arg196fs Pathogenic ★ same type
- CLCN4 p.Arg695fs Pathogenic ★ same type
- CLCN4 p.Asn309fs Pathogenic ★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/clcn4-p-phe319fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown